Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.
Exploration of the Drosophila buzzatii transposable element content suggests underestimation of repeats in Drosophila genomes.
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DOI：
10.1186/s12864-016-2648-8
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发表时间：
2016-05-10
期刊：
影响因子：
4.4
通讯作者：
Ruiz A
中科院分区：
文献类型：
--
作者：
Rius N;Guillén Y;Delprat A;Kapusta A;Feschotte C;Ruiz A
近年来，许多新的果蝇基因组已经使用新一代测序平台和组装方法进行了测序。转座元件(TES)是一种重复序列，经常会被错误组装，特别是在用短阅读进行测序的基因组中。因此，许多新基因组的流动部分没有得到详细的分析，也没有与用不同方法测序的其他基因组的流动部分进行比较，这可能有助于理解基因组和TE进化。这里我们比较了三个基因组的TE含量：D.buzzatii st-1，j-19和D.mojvensis。我们测序了一个新的布氏杜鹃基因组(j-19)，它补充了已发表的布氏杜鹃参考基因组(st-1)，并将它们的TE含量与莫氏杜鹃的TE含量进行了比较。我们发现与Sanger基因组相比，果蝇属NGS基因组中的TE序列被低估了。为了能够比较不同技术测序的基因组，我们开发了一种基于覆盖的方法，并将其应用于Buzzatii st-1和j-19基因组。白粉虫基因组的10.85%-11.16%由TES组成，TES占白粉虫j-19基因组的7%-7.5%，而TES占莫杰文氏丝虫基因组的15.35%。在这三个基因组中，氦电子是最丰富的目。根据基因组大小和TE含量的正相关关系，Buzzatii中的TES含量低于D.mojvensis中的TES。然而，TES本身并不能解释基因组大小的差异。TES聚集在布氏杜鹃和莫杰文氏杜鹃的点染色体和近端区域。我们还报告了Buzzatii和D.mojvensis X染色体上显著更高的TE密度，这在目前的模型下是不预期的。我们简单易用的校正方法使我们能够在Buzzatii st-1中鉴定出属于LTR-逆转座子超家族吉普赛的最近活跃的家族。本文的在线版本(doi：10.1186/s12864-0162648-8)包含补充材料，授权用户可以使用。
Many new Drosophila genomes have been sequenced in recent years using new-generation sequencing platforms and assembly methods. Transposable elements (TEs), being repetitive sequences, are often misassembled, especially in the genomes sequenced with short reads. Consequently, the mobile fraction of many of the new genomes has not been analyzed in detail or compared with that of other genomes sequenced with different methods, which could shed light into the understanding of genome and TE evolution. Here we compare the TE content of three genomes: D. buzzatii st-1, j-19, and D. mojavensis. We have sequenced a new D. buzzatii genome (j-19) that complements the D. buzzatii reference genome (st-1) already published, and compared their TE contents with that of D. mojavensis. We found an underestimation of TE sequences in Drosophila genus NGS-genomes when compared to Sanger-genomes. To be able to compare genomes sequenced with different technologies, we developed a coverage-based method and applied it to the D. buzzatii st-1 and j-19 genome. Between 10.85 and 11.16 % of the D. buzzatii st-1 genome is made up of TEs, between 7 and 7,5 % of D. buzzatii j-19 genome, while TEs represent 15.35 % of the D. mojavensis genome. Helitrons are the most abundant order in the three genomes. TEs in D. buzzatii are less abundant than in D. mojavensis, as expected according to the genome size and TE content positive correlation. However, TEs alone do not explain the genome size difference. TEs accumulate in the dot chromosomes and proximal regions of D. buzzatii and D. mojavensis chromosomes. We also report a significantly higher TE density in D. buzzatii and D. mojavensis X chromosomes, which is not expected under the current models. Our easy-to-use correction method allowed us to identify recently active families in D. buzzatii st-1 belonging to the LTR-retrotransposon superfamily Gypsy. The online version of this article (doi:10.1186/s12864-016-2648-8) contains supplementary material, which is available to authorized users.